They should have done a lot of things differently with servers in the very beginning.

They should have made our characters share a cross-server account name, allowing people to identify the player by account instead of character name (thereby preventing one RMT account from spamming with a hundred different characters).

They should have created a framework for cross-server play, like many western mmos have been experimenting with. Consider that we can group with random players from other servers during dungeons, but we can never meet or speak to those players in-game again. Meet someone new online or in real life that you want to play with? Pay $ to change server and say goodbye to all of your old in-game friends.

They should have experimented with different types of servers for different activities. Imagine if housing was on an entirely different server from your home world, and each housing server was shared among the general population. Access to housing would no longer be impossible on overpopulated servers and there wouldn't be dozens of empty housing wards on the lower population servers. Or how about a GLAMOUR server, where your character could temporarily migrate to access a glamour catalog for all of the armor designs you have unlocked? The glamour server would only load your current inventory and a massive wardrobe native to the server, ignoring all data for achievements and quests, thereby allowing the separate storage of data currently unmanageable by the native servers.

It's sad that Dragon Quest X was actually a lot more bold about how it handled server shards, and that was just a Wii game. Once they locked FFXIV into the same type of server system that traditional mmos had, they made it really hard to improve on how players are able to interact together.